Population_Manager Class Reference

Base class for all population managers. More...

#include <populationmanager.h>

Inheritance diagram for Population_Manager:

Public Member Functions
	Population_Manager (Landscape *L)
virtual	~Population_Manager (void)
void	SetNoProbes (int a_pn)
unsigned	GetLiveArraySize (int a_listindex)
	Gets the number of 'live' objects for a list index in the TheArray. More...
void	IncLiveArraySize (int a_listindex)
	Increments the number of 'live' objects for a list index in the TheArray. More...
virtual void	Catastrophe (int)
unsigned int	FarmAnimalCensus (unsigned int a_farm, unsigned int a_typeofanimal)
char *	SpeciesSpecificReporting (int a_species, int a_time)
char *	ProbeReport (int a_time)
char *	ProbeReportTimed (int a_time)
void	ImpactProbeReport (int a_Time)
bool	BeginningOfMonth ()
void	LOG (const char *fname)
int	SupplyStepSize ()
int	SupplySimW ()
int	SupplySimH ()
virtual void	Run (int NoTSteps)
virtual float	Probe (int ListIndex, probe_data *p_TheProbe)
virtual void	ImpactedProbe ()
int	SupplyListNameLength ()
TAnimal *	SupplyAnimalPtr (int a_index, int a_animal)
	Returns the pointer indexed by a_index and a_animal. Note NO RANGE CHECK. More...
unsigned	SupplyListIndexSize ()
unsigned	SupplyListSize (unsigned listindex)
bool	CheckXY (int l, int i)
	Debug method to test for out of bounds coordinates. More...
const char *	SupplyListName (int i)
bool	IsLast (unsigned listindex)
int	SupplyState (unsigned listindex, unsigned j)
virtual void	SupplyLocXY (unsigned listindex, unsigned j, int &x, int &y)
const char *	SupplyStateNames (int i)
unsigned	SupplyStateNamesLength ()
virtual void	DisplayLocations ()
int	ProbeFileInput (char *p_Filename, int p_ProbeNo)
TAnimal *	FindClosest (int x, int y, unsigned Type)
bool	OpenTheRipleysOutputProbe (string a_NWordFilename)
void	OpenTheAOROutputProbe (string a_AORFilename)
bool	OpenTheMonthlyRipleysOutputProbe ()
bool	OpenTheReallyBigProbe ()
virtual void	TheAOROutputProbe ()
virtual void	TheRipleysOutputProbe (FILE *a_prb)
virtual void	TheReallyBigOutputProbe ()
void	CloseTheMonthlyRipleysOutputProbe ()
virtual void	CloseTheRipleysOutputProbe ()
virtual void	CloseTheReallyBigOutputProbe ()
TTypesOfPopulation	GetPopulationType ()
int	GetSeasonNumber ()
	Get the season number. More...
void	LamdaDeath (int x, int y)
void	LamdaBirth (int x, int y)
void	LamdaBirth (int x, int y, int z)
void	LamdaClear ()
void	LamdaDumpOutput ()
virtual int	SupplyPegPosx (int)
virtual int	SupplyPegPosy (int)
virtual int	SupplyCovPosx (int)
virtual int	SupplyCovPosy (int)
virtual bool	OpenTheFledgelingProbe ()
virtual bool	OpenTheBreedingPairsProbe ()
virtual bool	OpenTheBreedingSuccessProbe ()
virtual void	BreedingPairsOutput (int)
virtual int	TheBreedingFemalesProbe (int)
virtual int	TheFledgelingProbe ()
virtual void	BreedingSuccessProbeOutput (double, int, int, int, int, int, int, int)
virtual int	TheBreedingSuccessProbe (int &, int &, int &, int &, int &, int &)
virtual void	FledgelingProbeOutput (int, int)
virtual void	TheGeneticProbe (unsigned, int, unsigned &)
virtual void	GeneticsResultsOutput (FILE *, unsigned)

Public Attributes
int	IndexArrayX [5][10000]
probe_data *	TheProbe [100]
int	SimH
int	SimW
unsigned	SimHH
unsigned	SimWH
char	m_SimulationName [255]
bool	ProbesSet
Landscape *	m_TheLandscape

Protected Member Functions
virtual bool	StepFinished ()
	Overrides the population manager StepFinished - there is no chance that hunters do not finish a step behaviour. More...
virtual void	DoFirst ()
virtual void	DoBefore ()
virtual void	DoAfter ()
virtual void	DoAlmostLast ()
virtual void	DoLast ()
void	EmptyTheArray ()
	Removes all objects from the TheArray by deleting them and clearing TheArray. More...
void	SortX (unsigned Type)
void	SortXIndex (unsigned Type)
void	SortY (unsigned Type)
void	SortState (unsigned Type)
void	SortStateR (unsigned Type)
unsigned	PartitionLiveDead (unsigned Type)
void	Shuffle_or_Sort (unsigned Type)
void	Shuffle (unsigned Type)
virtual void	Catastrophe ()

Protected Attributes
vector< unsigned >	m_LiveArraySize
int	m_NoProbes
AOR_Probe *	m_AOR_Probe
FILE *	m_GeneticsFile
FILE *	m_AlleleFreqsFile
FILE *	m_EasyPopRes
const char *	StateNames [100]
int	m_catastrophestartyear
int	m_StepSize
vector< TListOfAnimals >	TheArray
unsigned	StateNamesLength
const char *	m_ListNames [32]
unsigned	m_ListNameLength
FILE *	TestFile
FILE *	TestFile2
unsigned	BeforeStepActions [12]
int	m_SeasonNumber
	Holds the season number. Used when running goose and hunter sims. More...
TTypesOfPopulation	m_population_type
ofstream *	AOROutputPrb
FILE *	RipleysOutputPrb
FILE *	RipleysOutputPrb1
FILE *	RipleysOutputPrb2
FILE *	RipleysOutputPrb3
FILE *	RipleysOutputPrb4
FILE *	RipleysOutputPrb5
FILE *	RipleysOutputPrb6
FILE *	RipleysOutputPrb7
FILE *	RipleysOutputPrb8
FILE *	RipleysOutputPrb9
FILE *	RipleysOutputPrb10
FILE *	RipleysOutputPrb11
FILE *	RipleysOutputPrb12
FILE *	ReallyBigOutputPrb
long int	lamdagrid [2][257][257]

Detailed Description

Base class for all population managers.

The core of the handling of animal populations. All time-step code and most input/output is handled by this class and its descendents. This class effectively implements a state machine to facilitate simulation of animal behaviours and handle potential issues with concurrency. The PopulationManager class is never instantiated but must be used by deriving a descendent class.

Definition at line 424 of file populationmanager.h.

Constructor & Destructor Documentation

Population_Manager()

Population_Manager::Population_Manager

(

Landscape *

L

)

Constructor for the Population_Manager class

Definition at line 221 of file PopulationManager.cpp.

                                                      {
    // Keep a pointer to the landscape this population is in
    m_TheLandscape = L;
    // create 10 empty arrays as default, excess can be removed in descendent classes
    TListOfAnimals alist;
    TheArray.insert( TheArray.end(), 12, alist );
    // Set the simulation bounds
    SimH = m_TheLandscape->SupplySimAreaHeight();
    SimW = m_TheLandscape->SupplySimAreaWidth();
    SimHH = m_TheLandscape->SupplySimAreaHeight()/2;
    SimWH = m_TheLandscape->SupplySimAreaWidth()/2;
 
    // dww this is hardcoded limit of 12.
    // Needs fixing
    for (int i = 0; i < 12; i++) {
        // Set default BeforeStepActions
        BeforeStepActions[ i ] = 0;
        m_ListNames[ i ] = "Unknown";
        m_LiveArraySize.push_back( 0 );
    }
    // modify this if they need to in descendent classes
    StateNamesLength = 0; // initialise this variable.
    m_catastrophestartyear=-1; // Default is don't do this
#ifdef __LAMBDA_RECORD
    ofstream fout("LambdaGridOuput.txt", ios_base::out);  // open for writing
    fout.close();
    LamdaClear();
#endif
  if ( cfg_RipleysOutputMonthly_used.value() ) {
    OpenTheMonthlyRipleysOutputProbe();
  }
    if (cfg_AOROutput_used.value()) {
        OpenTheAOROutputProbe("AOR_Probe.txt"); 
    }
    // Ensure the GUI pointer is NULL in case we are not in GUI mode
#ifdef __ALMASS_VISUAL
    m_MainForm = NULL;
#endif
    m_SeasonNumber = 0;  // Ensure that we start in season number 0. Season number is incremented at day in year 183
}

References cfg_AOROutput_used, cfg_RipleysOutputMonthly_used, Landscape::SupplySimAreaHeight(), and CfgBool::value().

~Population_Manager()

Population_Manager::~Population_Manager ( void  )

virtual

Destructor for the Population_Manager class

Definition at line 266 of file PopulationManager.cpp.

                                              {
  // clean-up
  for ( unsigned i = 0; i < TheArray.size(); i++ ) {
    // if objects in the list need to be deleted:
    for ( unsigned j = 0; j < (unsigned) GetLiveArraySize(i); j++ ) {
      delete TheArray[ i ] [ j ];
    }
    // empty the array
    TheArray[ i ].clear();
    // --
  }
  if ( cfg_RipleysOutput_used.value() ) {
    CloseTheRipleysOutputProbe();
  }
 if ( cfg_RipleysOutputMonthly_used.value() ) {
    CloseTheMonthlyRipleysOutputProbe();
  }
  if ( cfg_ReallyBigOutput_used.value() ) {
    CloseTheReallyBigOutputProbe();
  }
  if (cfg_AOROutput_used.value()) delete m_AOR_Probe;
}

References cfg_AOROutput_used, cfg_ReallyBigOutput_used, cfg_RipleysOutput_used, cfg_RipleysOutputMonthly_used, and CfgBool::value().

Member Function Documentation

BeginningOfMonth()

bool Population_Manager::BeginningOfMonth

(

)

Is it the first day of the month?

Definition at line 1102 of file PopulationManager.cpp.

                                          {
  if ( m_TheLandscape->SupplyDayInMonth() == cfg_DayInMonth.value() ) return true;
  return false;
}

References cfg_DayInMonth, and CfgInt::value().

BreedingPairsOutput()

virtual void Population_Manager::BreedingPairsOutput ( int  )

inlinevirtual

Definition at line 641 of file populationmanager.h.

                                          {
    }

BreedingSuccessProbeOutput()

virtual void Population_Manager::BreedingSuccessProbeOutput ( double  , int  , int  , int  , int  , int  , int  , int    )

inlinevirtual

Definition at line 649 of file populationmanager.h.

                                                                                       {
    }

Catastrophe() [1/2]

void Population_Manager::Catastrophe ( )

protectedvirtual

This method MUST be overidden in descendent classes if this functionality is does not match with the animals requirements

Definition at line 1109 of file PopulationManager.cpp.

                                     {
    return;
}

Catastrophe() [2/2]

virtual void Population_Manager::Catastrophe ( int  )

inlinevirtual

Definition at line 440 of file populationmanager.h.

                                    {
    }

CheckXY()

bool Population_Manager::CheckXY	(	int	l,
		int	i
	)

Debug method to test for out of bounds coordinates.

Definition at line 1518 of file PopulationManager.cpp.

{
    if (TheArray[l][i]->Supply_m_Location_x() > 10000) return true;
    if (TheArray[l][i]->Supply_m_Location_y() > 10000) return true;
    if (TheArray[l][i]->Supply_m_Location_x() < 0) return true;
    if (TheArray[l][i]->Supply_m_Location_y() < 0) return true;
    return false;
}

CloseTheMonthlyRipleysOutputProbe()

void Population_Manager::CloseTheMonthlyRipleysOutputProbe

(

)

close the monthly probes

Definition at line 885 of file PopulationManager.cpp.

                                                           {
  fclose( RipleysOutputPrb1 );
  fclose( RipleysOutputPrb2 );
  fclose( RipleysOutputPrb3 );
  fclose( RipleysOutputPrb4 );
  fclose( RipleysOutputPrb5 );
  fclose( RipleysOutputPrb6 );
  fclose( RipleysOutputPrb7 );
  fclose( RipleysOutputPrb8 );
  fclose( RipleysOutputPrb9 );
  fclose( RipleysOutputPrb10 );
  fclose( RipleysOutputPrb11 );
  fclose( RipleysOutputPrb12 );
}

CloseTheReallyBigOutputProbe()

void Population_Manager::CloseTheReallyBigOutputProbe ( )

virtual

close the probe

Definition at line 904 of file PopulationManager.cpp.

                                                      {
  if ( ReallyBigOutputPrb != 0 )
    fclose( ReallyBigOutputPrb );
  ReallyBigOutputPrb=0;
}

CloseTheRipleysOutputProbe()

void Population_Manager::CloseTheRipleysOutputProbe ( )

virtual

close the probe

Definition at line 874 of file PopulationManager.cpp.

                                                    {
  if ( cfg_RipleysOutputMonthly_used.value() )
    fclose( RipleysOutputPrb );
  RipleysOutputPrb=NULL;
}

References cfg_RipleysOutputMonthly_used, and CfgBool::value().

DisplayLocations()

void Population_Manager::DisplayLocations ( )

virtual

Used to update the graphics when control is not returned to the ALMaSS_GUI between timesteps.

Definition at line 560 of file PopulationManager.cpp.

{
#ifdef __ALMASS_VISUAL
    m_MainForm->UpdateGraphics();
#endif
}

DoAfter()

void Population_Manager::DoAfter ( )

protectedvirtual

Can be used in descendent classes

Reimplemented in Rabbit_Population_Manager.

Definition at line 513 of file PopulationManager.cpp.

                                 {
  //TODO: Add your source code here
}

DoAlmostLast()

void Population_Manager::DoAlmostLast ( )

protectedvirtual

Can be used in descendent classes

Definition at line 522 of file PopulationManager.cpp.

                                      {
  //TODO: Add your source code here
}

DoBefore()

void Population_Manager::DoBefore ( )

protectedvirtual

Can be used in descendent classes

Reimplemented in Rabbit_Population_Manager.

Definition at line 328 of file PopulationManager.cpp.

                                  {
}

DoFirst()

void Population_Manager::DoFirst ( )

protectedvirtual

Can be used in descendent classes

Reimplemented in Rabbit_Population_Manager.

Definition at line 320 of file PopulationManager.cpp.

                                 {
}

DoLast()

void Population_Manager::DoLast ( )

protectedvirtual

Collects some data to describe the number of animals in each state at the end of the day

Reimplemented in Rabbit_Population_Manager.

Definition at line 530 of file PopulationManager.cpp.

                                {
 
/*
#ifdef __UNIX__
  for ( unsigned i = 0; i < 100; i++ ) {
    StateList.n[ i ] = 0;
  }
#else
  // Zero results
  for ( unsigned listindex = 0; listindex < m_ListNameLength; listindex++ ) {
    for ( unsigned i = 0; i < 100; i++ ) {
      Counts[ listindex ] [ i ] = 0;
    }
  }
#endif
  // How many animals in each state?
  for ( unsigned listindex = 0; listindex < TheArray.size(); listindex++ ) {
    unsigned size = (unsigned) TheArray[ listindex ].size();
    for ( unsigned j = 0; j < size; j++ ) {
#ifdef __UNIX__
      StateList.n[ TheArray[ listindex ] [ j ]->WhatState() ] ++;
#else
      Counts[ listindex ] [ TheArray[ listindex ] [ j ]->WhatState() ] ++;
#endif
    }
  }
*/
}

EmptyTheArray()

void Population_Manager::EmptyTheArray ( )

protected

Removes all objects from the TheArray by deleting them and clearing TheArray.

Sort TheArray w.r.t. the m_Location_x attribute

Definition at line 962 of file PopulationManager.cpp.

{
    for ( unsigned i = 0; i < TheArray.size(); i++ )
    {
        // if objects in the list need to be deleted:
        for (unsigned j = 0; j < (unsigned) TheArray[i].size(); j++)
        {
            delete TheArray[ i ] [ j ];
        }
        // empty the array
        TheArray[ i ].clear();
    }
}

FarmAnimalCensus()

unsigned int Population_Manager::FarmAnimalCensus	(	unsigned int	a_farm,
		unsigned int	a_typeofanimal
	)

Definition at line 1261 of file PopulationManager.cpp.

{
    unsigned int No = 0;
    unsigned sz = (unsigned)GetLiveArraySize( a_typeofanimal );
    for ( unsigned j = 0; j < sz; j++ ) 
    {
        if (a_farm == TheArray[ a_typeofanimal ] [ j ]->SupplyFarmOwnerRef()) No++;
    }
    return No;
}

FindClosest()

TAnimal * Population_Manager::FindClosest	(	int	x,
		int	y,
		unsigned	Type
	)

Finds the closest individual to an x,y point

Definition at line 937 of file PopulationManager.cpp.

                                                                       {
  int distance = 100000000;
  TAnimal * TA = NULL;
  int dx, dy, d;
  for (unsigned j = 0; j < (unsigned)GetLiveArraySize( Type ); j++) {
    dx = TheArray[ Type ] [ j ]->Supply_m_Location_x();
    dy = TheArray[ Type ] [ j ]->Supply_m_Location_y();
    dx = ( dx - x );
    dx *= dx;
    dy = ( dy - y );
 
    dy *= dy;
    d = dx + dy;
    if ( d < distance ) {
      distance = d;
      TA = TheArray[ Type ] [ j ];
    }
  }
  return TA;
}

References TAnimal::Supply_m_Location_x().

FledgelingProbeOutput()

virtual void Population_Manager::FledgelingProbeOutput ( int  , int    )

inlinevirtual

Definition at line 654 of file populationmanager.h.

                                                 {
    }

GeneticsResultsOutput()

virtual void Population_Manager::GeneticsResultsOutput ( FILE *  , unsigned    )

inlinevirtual

Definition at line 658 of file populationmanager.h.

                                                         {
    }

GetLiveArraySize()

unsigned Population_Manager::GetLiveArraySize ( int  a_listindex )

inline

Gets the number of 'live' objects for a list index in the TheArray.

Definition at line 433 of file populationmanager.h.

                                               {
        return m_LiveArraySize[a_listindex];
    }

References m_LiveArraySize.

Referenced by Rabbit_Warren::CalcDisease().

GetPopulationType()

TTypesOfPopulation Population_Manager::GetPopulationType ( )

inline

Definition at line 576 of file populationmanager.h.

{ return m_population_type; }

References m_population_type.

GetSeasonNumber()

int Population_Manager::GetSeasonNumber ( )

inline

Get the season number.

Definition at line 578 of file populationmanager.h.

{ return m_SeasonNumber; }

References m_SeasonNumber.

ImpactedProbe()

void Population_Manager::ImpactedProbe ( )

virtual

Special pesticide related probe. Overidden in descendent classes

Definition at line 672 of file PopulationManager.cpp.

                                        {
 
}

ImpactProbeReport()

void Population_Manager::ImpactProbeReport

(

int

a_Time

)

Special probe

Definition at line 1321 of file PopulationManager.cpp.

                                                       {
 
  for ( int ProbeNo = 0; ProbeNo < 1; ProbeNo++ ) {
    // See if we need to record/update this one
    // if time/months/years ==0 or every time
    if ( ( TheProbe[ ProbeNo ]->m_ReportInterval == 3 )
         || ( ( TheProbe[ ProbeNo ]->m_ReportInterval == 2 ) && ( BeginningOfMonth() ) )
         || ( ( TheProbe[ ProbeNo ]->m_ReportInterval == 1 ) && ( a_Time % 365 == 0 ) ) ) {
             ImpactedProbe();
    }
  }
}

IncLiveArraySize()

void Population_Manager::IncLiveArraySize ( int  a_listindex )

inline

Increments the number of 'live' objects for a list index in the TheArray.

Definition at line 437 of file populationmanager.h.

                                           {
        m_LiveArraySize[a_listindex]++;
    }

References m_LiveArraySize.

IsLast()

bool Population_Manager::IsLast ( unsigned  listindex )

inline

Definition at line 481 of file populationmanager.h.

                                    {
        if (TheArray[listindex].size() > 1) return false; else
            return true;
    }

References TheArray.

LamdaBirth() [1/2]

void Population_Manager::LamdaBirth ( int  x, int  y  )

inline

Definition at line 603 of file populationmanager.h.

                                  {
        lamdagrid[0][x / __lgridsize][y / __lgridsize]++;
    }

References lamdagrid.

LamdaBirth() [2/2]

void Population_Manager::LamdaBirth ( int  x, int  y, int  z  )

inline

Definition at line 606 of file populationmanager.h.

                                         {
        lamdagrid[0][x / __lgridsize][y / __lgridsize] += z;
    }

References lamdagrid.

LamdaClear()

void Population_Manager::LamdaClear ( )

inline

Definition at line 609 of file populationmanager.h.

                      {
        for (int i = 0; i < 257; i++) {
            for (int j = 0; j < 257; j++) {
                lamdagrid[0][i][j] = 0;
                lamdagrid[1][i][j] = 0;
            }
        }
    }

References lamdagrid.

LamdaDeath()

void Population_Manager::LamdaDeath ( int  x, int  y  )

inline

Definition at line 599 of file populationmanager.h.

                                  {
        // inlined for speed
        lamdagrid[1][x / __lgridsize][y / __lgridsize]++;
    }

References lamdagrid.

LamdaDumpOutput()

void Population_Manager::LamdaDumpOutput

(

)

Special probe

Definition at line 657 of file PopulationManager.cpp.

                                         {
   ofstream fout("LambdaGridOuput.txt", ios_base::app);  // open for writing
   for (int i=0; i<257; i++ ) {
       for (int j=0; j<257; j++) {
           fout << lamdagrid[0][i][j] << "\t" << lamdagrid[1][i][j] << endl;
       }
   }
   //fout << "NEXT" << endl;
   fout.close();
}

LOG()

void Population_Manager::LOG

(

const char *

fname

)

Debug function used to log whatever is needed - this is just a place to write whatever is needed at the time - so contents vary

Definition at line 294 of file PopulationManager.cpp.

                                                {
  FILE * PFile = fopen(fname, "w" );
  if (PFile) {
      m_TheLandscape->Warn("PopulationManager::LOG - Could not open file ",fname);
      exit(0);
  }
  AnimalPosition AP;
  for ( unsigned listindex = 0; listindex < TheArray.size(); listindex++ ) {
#ifndef __BCB__
    fprintf( PFile, "%s :\n", m_ListNames[ listindex ] );
#else
    fprintf( PFile, "%s :\n", m_ListNames[ listindex ].c_str() );
#endif
    for ( unsigned j = 0; j < (unsigned) m_LiveArraySize[listindex]; j++ ) {
      AP = TheArray[ listindex ] [ j ]->SupplyPosition();
      fprintf( PFile, "%i %i %i\n", j, AP.m_x, AP.m_y );
    }
  }
  fclose( PFile );
}

References AnimalPosition::m_x, and AnimalPosition::m_y.

OpenTheAOROutputProbe()

void Population_Manager::OpenTheAOROutputProbe

(

string

a_AORFilename

)

open the AOR Grid probe

Definition at line 771 of file PopulationManager.cpp.

                                                                   {
    m_AOR_Probe = new AOR_Probe(this, m_TheLandscape, a_AORFilename); 
}

OpenTheBreedingPairsProbe()

virtual bool Population_Manager::OpenTheBreedingPairsProbe ( )

inlinevirtual

Definition at line 635 of file populationmanager.h.

                                             {
        return false;
    }

OpenTheBreedingSuccessProbe()

virtual bool Population_Manager::OpenTheBreedingSuccessProbe ( )

inlinevirtual

Definition at line 638 of file populationmanager.h.

                                               {
        return false;
    }

OpenTheFledgelingProbe()

virtual bool Population_Manager::OpenTheFledgelingProbe ( )

inlinevirtual

Definition at line 632 of file populationmanager.h.

                                          {
        return false;
    }

OpenTheMonthlyRipleysOutputProbe()

bool Population_Manager::OpenTheMonthlyRipleysOutputProbe

(

)

open 12 ripley output probles, one for each month

Definition at line 778 of file PopulationManager.cpp.

                                                          {
  RipleysOutputPrb1 = fopen("RipleyOutput_Jan.txt", "w" );
  if ( !RipleysOutputPrb1 ) {
    g_msg->Warn( WARN_FILE, "Population_Manager::OpenTheRipleysOutputProbe(): ""Unable to open probe file",
         cfg_RipleysOutput_filename.value() );
    exit( 1 );
  }
  RipleysOutputPrb2 = fopen("RipleyOutput_Feb.txt", "w" );
  if ( !RipleysOutputPrb2 ) {
    g_msg->Warn( WARN_FILE, "Population_Manager::OpenTheRipleysOutputProbe(): ""Unable to open probe file",
         cfg_RipleysOutput_filename.value() );
    exit( 1 );
  }
  RipleysOutputPrb3 = fopen("RipleyOutput_Mar.txt", "w" );
  if ( !RipleysOutputPrb3 ) {
    g_msg->Warn( WARN_FILE, "Population_Manager::OpenTheRipleysOutputProbe(): ""Unable to open probe file",
         cfg_RipleysOutput_filename.value() );
    exit( 1 );
  }
  RipleysOutputPrb4 = fopen("RipleyOutput_Apr.txt", "w" );
  if ( !RipleysOutputPrb4 ) {
    g_msg->Warn( WARN_FILE, "Population_Manager::OpenTheRipleysOutputProbe(): ""Unable to open probe file",
         cfg_RipleysOutput_filename.value() );
    exit( 1 );
  }
  RipleysOutputPrb5 = fopen("RipleyOutput_May.txt", "w" );
  if ( !RipleysOutputPrb5 ) {
    g_msg->Warn( WARN_FILE, "Population_Manager::OpenTheRipleysOutputProbe(): ""Unable to open probe file",
         cfg_RipleysOutput_filename.value() );
    exit( 1 );
  }
  RipleysOutputPrb6 = fopen("RipleyOutput_Jun.txt", "w" );
  if ( !RipleysOutputPrb6 ) {
    g_msg->Warn( WARN_FILE, "Population_Manager::OpenTheRipleysOutputProbe(): ""Unable to open probe file",
         cfg_RipleysOutput_filename.value() );
    exit( 1 );
  }
  RipleysOutputPrb7 = fopen("RipleyOutput_Jul.txt", "w" );
  if ( !RipleysOutputPrb7 ) {
    g_msg->Warn( WARN_FILE, "Population_Manager::OpenTheRipleysOutputProbe(): ""Unable to open probe file",
         cfg_RipleysOutput_filename.value() );
    exit( 1 );
  }
  RipleysOutputPrb8 = fopen("RipleyOutput_Aug.txt", "w" );
  if ( !RipleysOutputPrb8 ) {
    g_msg->Warn( WARN_FILE, "Population_Manager::OpenTheRipleysOutputProbe(): ""Unable to open probe file",
         cfg_RipleysOutput_filename.value() );
    exit( 1 );
  }
  RipleysOutputPrb9 = fopen("RipleyOutput_Sep.txt", "w" );
  if ( !RipleysOutputPrb9 ) {
    g_msg->Warn( WARN_FILE, "Population_Manager::OpenTheRipleysOutputProbe(): ""Unable to open probe file",
         cfg_RipleysOutput_filename.value() );
    exit( 1 );
  }
  RipleysOutputPrb10 = fopen("RipleyOutput_Oct.txt", "w" );
  if ( !RipleysOutputPrb10 ) {
    g_msg->Warn( WARN_FILE, "Population_Manager::OpenTheRipleysOutputProbe(): ""Unable to open probe file",
         cfg_RipleysOutput_filename.value() );
    exit( 1 );
  }
  RipleysOutputPrb11 = fopen("RipleyOutput_Nov.txt", "w" );
  if ( !RipleysOutputPrb11 ) {
    g_msg->Warn( WARN_FILE, "Population_Manager::OpenTheRipleysOutputProbe(): ""Unable to open probe file",
         cfg_RipleysOutput_filename.value() );
    exit( 1 );
  }
  RipleysOutputPrb12 = fopen("RipleyOutput_Dec.txt", "w" );
  if ( !RipleysOutputPrb12 ) {
    g_msg->Warn( WARN_FILE, "Population_Manager::OpenTheRipleysOutputProbe(): ""Unable to open probe file",
         cfg_RipleysOutput_filename.value() );
    exit( 1 );
  }
  return true;
}

References cfg_RipleysOutput_filename, g_msg, CfgStr::value(), MapErrorMsg::Warn(), and WARN_FILE.

OpenTheReallyBigProbe()

bool Population_Manager::OpenTheReallyBigProbe

(

)

open the probe

Definition at line 859 of file PopulationManager.cpp.

                                               {
  ReallyBigOutputPrb = fopen(cfg_ReallyBigOutput_filename.value(), "w" );
  if ( !ReallyBigOutputPrb ) {
    g_msg->Warn( WARN_FILE, "Population_Manager::OpenTheRipleysOutputProbe(): ""Unable to open probe file",
         cfg_ReallyBigOutput_filename.value() );
    exit( 1 );
  }
  return true;
}

References cfg_ReallyBigOutput_filename, g_msg, CfgStr::value(), MapErrorMsg::Warn(), and WARN_FILE.

OpenTheRipleysOutputProbe()

bool Population_Manager::OpenTheRipleysOutputProbe

(

string

a_NWordFilename

)

open the Ripley probe

Definition at line 757 of file PopulationManager.cpp.

                                                                         {
    RipleysOutputPrb = fopen(cfg_RipleysOutput_filename.value(), "w");
    if (!RipleysOutputPrb) {
        g_msg->Warn(WARN_FILE, "Population_Manager::OpenTheRipleysOutputProbe(): ""Unable to open probe file",
            cfg_RipleysOutput_filename.value());
        exit(1);
    }
    return true;
}

References cfg_RipleysOutput_filename, g_msg, CfgStr::value(), MapErrorMsg::Warn(), and WARN_FILE.

Referenced by Rabbit_Population_Manager::Rabbit_Population_Manager().

PartitionLiveDead()

unsigned Population_Manager::PartitionLiveDead ( unsigned  Type )

protected

Sort TheArray w.r.t. the current state attribute in reverse order

Definition at line 1015 of file PopulationManager.cpp.

                                                            {
    auto it = partition(TheArray[Type].begin(), TheArray[Type].begin() + m_LiveArraySize[Type], CompareStateAlive());
    // it now points at the first dead element
    // the number of live ones before it is it-TheArray[Type].begin(). This is the new vector size for live animals.
    return unsigned(it - TheArray[Type].begin());
}

Probe()

float Population_Manager::Probe ( int  ListIndex, probe_data *  p_TheProbe  )

virtual

Default data probe. Rarely used in actuality but always available

Definition at line 680 of file PopulationManager.cpp.

                                                                        {
    // Counts through the list and goes through each area to see if the animal
    // is standing there and if the farm, veg or element conditions are met
    AnimalPosition Sp;
    float NumberSk = 0;
    // Four possibilites
    // either NoVegTypes or NoElementTypes or NoFarmTypes is >0 or all==0
    if ( p_TheProbe->m_NoFarms != 0 ) {
        for (unsigned j = 0; j < (unsigned)GetLiveArraySize( ListIndex ); j++) {
            Sp = TheArray[ ListIndex ] [ j ]->SupplyPosition();
            unsigned Farm = TheArray[ ListIndex ] [ j ]->SupplyFarmOwnerRef();
            for ( unsigned i = 0; i < p_TheProbe->m_NoAreas; i++ ) {
                if ( ( Sp.m_x >= p_TheProbe->m_Rect[ i ].m_x1 ) && ( Sp.m_y >= p_TheProbe->m_Rect[ i ].m_y1 )
                        && ( Sp.m_x <= p_TheProbe->m_Rect[ i ].m_x2 ) && ( Sp.m_y <= p_TheProbe->m_Rect[ i ].m_y2 ) )
                for ( unsigned k = 0; k < p_TheProbe->m_NoFarms; k++ ) {
                    if ( p_TheProbe->m_RefFarms[ k ] == Farm )
                    NumberSk++; // it is in the square so increment number
                }
 
            }
    }
    } else if ( p_TheProbe->m_NoEleTypes != 0 ) {
        for (unsigned j = 0; j < (unsigned)GetLiveArraySize( ListIndex ); j++) {
      Sp = TheArray[ ListIndex ] [ j ]->SupplyPosition();
      for ( unsigned i = 0; i < p_TheProbe->m_NoAreas; i++ ) {
        if ( ( Sp.m_x >= p_TheProbe->m_Rect[ i ].m_x1 ) && ( Sp.m_y >= p_TheProbe->m_Rect[ i ].m_y1 )
             && ( Sp.m_x <= p_TheProbe->m_Rect[ i ].m_x2 ) && ( Sp.m_y <= p_TheProbe->m_Rect[ i ].m_y2 ) )
               for ( unsigned k = 0; k < p_TheProbe->m_NoEleTypes; k++ ) {
                 if ( p_TheProbe->m_RefEle[ k ] == Sp.m_EleType )
                   NumberSk++; // it is in the square so increment number
               }
      }
    }
    } else {
    if ( p_TheProbe->m_NoVegTypes != 0 ) {
        for (unsigned j = 0; j < (unsigned)GetLiveArraySize( ListIndex ); j++) {
        Sp = TheArray[ ListIndex ] [ j ]->SupplyPosition();
 
        for ( unsigned i = 0; i < p_TheProbe->m_NoAreas; i++ ) {
          if ( ( Sp.m_x >= p_TheProbe->m_Rect[ i ].m_x1 ) && ( Sp.m_y >= p_TheProbe->m_Rect[ i ].m_y1 )
               && ( Sp.m_x <= p_TheProbe->m_Rect[ i ].m_x2 ) && ( Sp.m_y <= p_TheProbe->m_Rect[ i ].m_y2 ) ) {
                 for ( unsigned k = 0; k < p_TheProbe->m_NoVegTypes; k++ ) {
                   if ( p_TheProbe->m_RefVeg[ k ] == Sp.m_VegType )
                     NumberSk++; // it is in the square so increment number
                 }
          }
        }
      }
    } else // both must be zero
    {
        unsigned sz = (unsigned)GetLiveArraySize( ListIndex );
        // It is worth checking whether we have a total dump of all individuals
        // if so don't bother with asking each where it is
        if (p_TheProbe->m_NoAreas==1) {
            if ((p_TheProbe->m_Rect[0].m_x1==0) && (p_TheProbe->m_Rect[0].m_y1==0) && (p_TheProbe->m_Rect[0].m_x2==(unsigned)SimW) &&
                (p_TheProbe->m_Rect[0].m_y2==(unsigned)SimH)) {
                    return (float) sz;
            }
        }
        // Asking for a subset - need to test them all
        for ( unsigned j = 0; j < sz; j++ ) {
            Sp = TheArray[ ListIndex ] [ j ]->SupplyPosition();
            for ( unsigned i = 0; i < p_TheProbe->m_NoAreas; i++ ) {
                if ( ( Sp.m_x >= p_TheProbe->m_Rect[ i ].m_x1 ) && ( Sp.m_y >= p_TheProbe->m_Rect[ i ].m_y1 )
                       && ( Sp.m_x <= p_TheProbe->m_Rect[ i ].m_x2 ) && ( Sp.m_y <= p_TheProbe->m_Rect[ i ].m_y2 ) )
                        NumberSk++; // it is in the square so increment number
            }
        }
    }
    }
    return NumberSk;
}

References AnimalPosition::m_EleType, probe_data::m_NoAreas, probe_data::m_NoEleTypes, probe_data::m_NoFarms, probe_data::m_NoVegTypes, probe_data::m_Rect, probe_data::m_RefEle, probe_data::m_RefFarms, probe_data::m_RefVeg, AnimalPosition::m_VegType, AnimalPosition::m_x, rectangle::m_x1, rectangle::m_x2, AnimalPosition::m_y, rectangle::m_y1, and rectangle::m_y2.

ProbeFileInput()

int Population_Manager::ProbeFileInput	(	char *	p_Filename,
		int	p_ProbeNo
	)

Default probe file input

Definition at line 574 of file PopulationManager.cpp.

                                                                         {
  FILE * PFile;
  int data = 0;
  int data2 = 0;
  char S[ 255 ];
  PFile = fopen(p_Filename, "r" );
  if ( !PFile ) {
    m_TheLandscape->Warn( "Population Manager - cannot open Probe File ", p_Filename );
    exit( 0 );
  }
  fgets( S, 255, PFile ); // dummy line
  fgets( S, 255, PFile ); // dummy line
  fscanf( PFile, "%d\n", & data ); // Reporting interval
  TheProbe[ p_ProbeNo ]->m_ReportInterval = data;
  fgets( S, 255, PFile ); // dummy line
  fscanf( PFile, "%d\n", & data ); // Write to file
  if ( data == 0 ) TheProbe[ p_ProbeNo ]->m_FileRecord = false; else
    TheProbe[ p_ProbeNo ]->m_FileRecord = true;
  fgets( S, 255, PFile ); // dummy line
  for ( int i = 0; i < 10; i++ ) {
    fscanf( PFile, "%d", & data );
    if ( data > 0 ) TheProbe[ p_ProbeNo ]->m_TargetTypes[ i ] = true; else
      TheProbe[ p_ProbeNo ]->m_TargetTypes[ i ] = false;
  }
 
  fgets( S, 255, PFile ); // dummy line
  fgets( S, 255, PFile ); // dummy line
  fscanf( PFile, "%d", & data );
  TheProbe[ p_ProbeNo ]->m_NoAreas = data;
  fgets( S, 255, PFile ); // dummy line
  fgets( S, 255, PFile ); // dummy line
  fscanf( PFile, "%d", & data2 ); // No References areas
  fgets( S, 255, PFile ); // dummy line
  fgets( S, 255, PFile ); // dummy line
  fscanf( PFile, "%d", & data ); // Type reference for probe
  if ( data == 1 ) TheProbe[ p_ProbeNo ]->m_NoEleTypes = data2; else
    TheProbe[ p_ProbeNo ]->m_NoEleTypes = 0;
  if ( data == 2 ) TheProbe[ p_ProbeNo ]->m_NoVegTypes = data2; else
    TheProbe[ p_ProbeNo ]->m_NoVegTypes = 0;
  if ( data == 3 ) TheProbe[ p_ProbeNo ]->m_NoFarms = data2; else
    TheProbe[ p_ProbeNo ]->m_NoFarms = 0;
  fgets( S, 255, PFile ); // dummy line
  fgets( S, 255, PFile ); // dummy line
  // Now read in the areas data
  for ( int i = 0; i < 10; i++ ) {
    fscanf( PFile, "%d", & data );
    TheProbe[ p_ProbeNo ]->m_Rect[ i ].m_x1 = data;
    fscanf( PFile, "%d", & data );
    TheProbe[ p_ProbeNo ]->m_Rect[ i ].m_y1 = data;
    fscanf( PFile, "%d", & data );
    TheProbe[ p_ProbeNo ]->m_Rect[ i ].m_x2 = data;
    fscanf( PFile, "%d", & data );
    TheProbe[ p_ProbeNo ]->m_Rect[ i ].m_y2 = data;
  }
  fgets( S, 255, PFile ); // dummy line
  fgets( S, 255, PFile ); // dummy line
  if ( TheProbe[ p_ProbeNo ]->m_NoVegTypes > 0 ) {
    for ( int i = 0; i < 25; i++ ) {
      fscanf( PFile, "%d", & data );
      if ( data != 999 )
        TheProbe[ p_ProbeNo ]->m_RefVeg[ i ] = m_TheLandscape->TranslateVegTypes( data );
    }
  } else if ( TheProbe[ p_ProbeNo ]->m_NoFarms > 0 ) {
    for ( int i = 0; i < 25; i++ ) {
      fscanf( PFile, "%d", & data );
      if ( data != 999 )
        TheProbe[ p_ProbeNo ]->m_RefFarms[ i ] = data;
    }
  } else {
    for ( int i = 0; i < 25; i++ ) {
      fscanf( PFile, "%d", & data );
      if ( data != 999 ) TheProbe[ p_ProbeNo ]->m_RefEle[ i ] = m_TheLandscape->TranslateEleTypes( data );
    }
  }
  fclose( PFile );
  return data2; // number of data references
}

ProbeReport()

char * Population_Manager::ProbeReport

(

int

a_time

)

Definition at line 1273 of file PopulationManager.cpp.

                                                {
 
  int No;
  char str[100]; // 100 out to be enough!!
  strcpy(g_str,"");
  for ( int ProbeNo = 0; ProbeNo < m_NoProbes; ProbeNo++ ) {
    No = 0;
    // See if we need to record/update this one
    // if time/months/years ==0 or every time
    if ( ( TheProbe[ ProbeNo ]->m_ReportInterval == 3 )
         || ( ( TheProbe[ ProbeNo ]->m_ReportInterval == 2 ) && ( BeginningOfMonth() ) )
         || ( ( TheProbe[ ProbeNo ]->m_ReportInterval == 1 ) && ( Time % 365 == 0 ) ) ) {
           // Goes through each area and sends a value to OutputForm
           unsigned Index = SupplyListIndexSize();
           for ( unsigned listindex = 0; listindex < Index; listindex++ ) {
             if ( TheProbe[ ProbeNo ]->m_TargetTypes[ listindex ] )
               No += (int) Probe( listindex, TheProbe[ ProbeNo ] );
           }
           TheProbe[ ProbeNo ]->FileOutput( No, Time, ProbeNo );
            sprintf(str," %d ", No );
            strcat(g_str,str);
    }
  }
  return g_str;
}

References g_str.

ProbeReportTimed()

char * Population_Manager::ProbeReportTimed

(

int

a_time

)

Definition at line 1300 of file PopulationManager.cpp.

                                                    {
    int No;
    char str[100]; // 100 ought to be enough!!
    strcpy(g_str,"");
    for ( int ProbeNo = 0; ProbeNo < m_NoProbes; ProbeNo++ ) {
    No = 0;
    unsigned Index = SupplyListIndexSize();
    for ( unsigned listindex = 0; listindex < Index; listindex++ ) {
        if ( TheProbe[ ProbeNo ]->m_TargetTypes[ listindex ] ) No += (int) Probe( listindex, TheProbe[ ProbeNo ] );
    }
    TheProbe[ ProbeNo ]->FileOutput( No, Time, ProbeNo );
    sprintf(str," %d ", No );
    strcat(g_str,str);
  }
  return g_str;
}

References g_str.

Run()

void Population_Manager::Run ( int  NoTSteps )

virtual

This is the main scheduling method for the population manager.
Note the structure of Shuffle_or_Sort(), DoFirst(), BeginStep, DoBefore(), Step looping until all are finished, DoAfter(), DoAlmostLast(), EndStep, DoLast().

Can do multiple time-steps here inside one landscape time-step (a day). This is used in the roe deer model to provide 10 minute behavioural time-steps.

It is necessary to remove any dead animals before the timestep starts. It is possible that animals are killed after their population manager Run method has been executed. This is the case with geese and hunters. Checking death first prevents this becomming a problem.

Definition at line 337 of file PopulationManager.cpp.

                                           {
  for ( int TSteps = 0; TSteps < NoTSteps; TSteps++ )
  {
      unsigned size2;
      unsigned size1 =  (unsigned) TheArray.size();
      for ( unsigned listindex = 0; listindex < size1; listindex++ )
      {
          // Must check each object in the list for m_CurrentStateNo==-1
          m_LiveArraySize[listindex] = PartitionLiveDead(listindex);
      }
#ifdef __ALMASS_VISUAL
      if (m_MainForm!=NULL)
      {
          int n = 0;
          for ( unsigned listindex = 0; listindex < size1; listindex++ ) n += (int) m_LiveArraySize[ listindex ];
          //if (n>0) DisplayLocations();
      }
#endif
      // begin step actions ...
      // set all stepdone to false.... is this really necessary??
      for ( unsigned listindex = 0; listindex < size1; listindex++ )
      {
          size2 = (unsigned) GetLiveArraySize(listindex);
          for ( unsigned j = 0; j < size2; j++ )
          {
              TheArray[ listindex ] [ j ]->SetStepDone( false );
          }
      }
 
      for ( unsigned listindex = 0; listindex < size1; listindex++ ) {
          // Call the Shuffle/Sort procedures
          Shuffle_or_Sort( listindex );
      }
      // Need to check if Ripleys Statistic needs to be saved
      if (cfg_RipleysOutput_used.value()) {
          int Year = m_TheLandscape->SupplyYearNumber();
          if (Year >= cfg_RipleysOutputFirstYear.value()) {
              if (Year % cfg_RipleysOutput_interval.value() == 0) {
                  int day = m_TheLandscape->SupplyDayInYear();
                  if (cfg_RipleysOutput_day.value() == day) {
                      // Do the Ripley Probe
                      TheRipleysOutputProbe(RipleysOutputPrb);
                  }
              }
          }
      }
      // Need to check if AOR output needs to be saved
      if (cfg_AOROutput_used.value()) {
          int Year = m_TheLandscape->SupplyYearNumber();
          if (Year >= cfg_AOROutputFirstYear.value()) {
              if (Year % cfg_AOROutput_interval.value() == 0) {
                  int day = m_TheLandscape->SupplyDayInYear();
                  if (cfg_AOROutput_day.value() == day) {
                      // Do the AOR Probe
                      TheAOROutputProbe();
                  }
              }
          }
      }
      // Need to check if Monthly Ripleys Statistic needs to be saved
    if ( cfg_RipleysOutputMonthly_used.value() ) {
        if (m_TheLandscape->SupplyDayInMonth()==1) {
            int Year = m_TheLandscape->SupplyYearNumber();
            if (Year>=cfg_RipleysOutputFirstYear.value()) {
                if ( Year % cfg_RipleysOutput_interval.value() == 0 ) {
                    int month = m_TheLandscape->SupplyMonth();
                    // Do the Ripley Probe
                    switch (month) {
                        case 1: TheRipleysOutputProbe( RipleysOutputPrb1 );
                            break;
                        case 2: TheRipleysOutputProbe( RipleysOutputPrb2 );
                            break;
                        case 3: TheRipleysOutputProbe( RipleysOutputPrb3 );
                            break;
                        case 4: TheRipleysOutputProbe( RipleysOutputPrb4 );
                            break;
                        case 5: TheRipleysOutputProbe( RipleysOutputPrb5 );
                            break;
                        case 6: TheRipleysOutputProbe( RipleysOutputPrb6 );
                            break;
                        case 7: TheRipleysOutputProbe( RipleysOutputPrb7 );
                            break;
                        case 8: TheRipleysOutputProbe( RipleysOutputPrb8 );
                            break;
                        case 9: TheRipleysOutputProbe( RipleysOutputPrb9 );
                            break;
                        case 10: TheRipleysOutputProbe( RipleysOutputPrb10 );
                            break;
                        case 11: TheRipleysOutputProbe( RipleysOutputPrb11 );
                            break;
                        case 12: TheRipleysOutputProbe( RipleysOutputPrb12 );
                            break;
                    }
                }
            }
        }
    }
    // Need to check if Really Big Probe needs to be saved
    if ( cfg_ReallyBigOutput_used.value() ) {
      int Year = m_TheLandscape->SupplyYearNumber();
      if (Year>=cfg_ReallyBigOutputFirstYear.value()) {
          if ( Year % cfg_ReallyBigOutput_interval.value() == 0 ) {
            int day = m_TheLandscape->SupplyDayInYear();
            if (( cfg_ReallyBigOutput_day1.value() == day )|| ( cfg_ReallyBigOutput_day2.value() == day )|| ( cfg_ReallyBigOutput_day3.value() == day )|| ( cfg_ReallyBigOutput_day4.value() == day )||( cfg_ReallyBigOutput_day1.value() == -1 ))
            {
              // Do the Ripley Probe
              TheReallyBigOutputProbe();
            }
          }
        }
    }
    int yr=m_TheLandscape->SupplyYearNumber();
    if ( yr > cfg_CatastropheEventStartYear.value() ) {
        if (m_catastrophestartyear==-1) m_catastrophestartyear=yr;
        Catastrophe(); // This method must be overidden in descendent classes
    }
    DoFirst();
    // call the begin-step-method of all objects
    for ( unsigned listindex = 0; listindex < size1; listindex++ ) {
        size2 = (unsigned)GetLiveArraySize( listindex );
        for (unsigned j = 0; j < size2; j++)
        TheArray[ listindex ] [ j ]->BeginStep();
    }
    DoBefore();
    // call the step-method of all objects
    do {
      for ( unsigned listindex = 0; listindex < size1; listindex++ ) {
          size2 = (unsigned)GetLiveArraySize( listindex );
          for (unsigned j = 0; j < size2; j++) {
          TheArray[ listindex ] [ j ]->Step();
        }
      } // for listindex
    } while ( !StepFinished() );
    DoAfter();
    // call the end-step-method of all objects
    for ( unsigned listindex = 0; listindex < size1; listindex++ ) {
        size2 = (unsigned)GetLiveArraySize( listindex );
        for (unsigned j = 0; j < size2; j++) {
        TheArray[ listindex ] [ j ]->EndStep();
      }
    }
    // ----------------
    // end of this step actions
    // For each animal list
    DoAlmostLast();
 
DoLast();
  } // End of time step loop
}

References cfg_AOROutput_day, cfg_AOROutput_interval, cfg_AOROutput_used, cfg_AOROutputFirstYear, cfg_CatastropheEventStartYear, cfg_ReallyBigOutput_day1, cfg_ReallyBigOutput_day2, cfg_ReallyBigOutput_day3, cfg_ReallyBigOutput_day4, cfg_ReallyBigOutput_interval, cfg_ReallyBigOutput_used, cfg_ReallyBigOutputFirstYear, cfg_RipleysOutput_day, cfg_RipleysOutput_interval, cfg_RipleysOutput_used, cfg_RipleysOutputFirstYear, cfg_RipleysOutputMonthly_used, CfgInt::value(), and CfgBool::value().

SetNoProbes()

void Population_Manager::SetNoProbes ( int  a_pn )

inline

Definition at line 431 of file populationmanager.h.

{ m_NoProbes = a_pn; }

References m_NoProbes.

Shuffle()

void Population_Manager::Shuffle ( unsigned  Type )

protected

Run once through the list swapping randomly chosen elements

Definition at line 1055 of file PopulationManager.cpp.

                                                {
    unsigned s = (unsigned)GetLiveArraySize( Type );
  for ( unsigned i = 0; i < s; i++ ) {
    TAnimal * temp;
    unsigned a = random( s );
    unsigned b = random( s );
    temp = TheArray[ Type ] [ a ];
    TheArray[ Type ] [ a ] = TheArray[ Type ] [ b ];
    TheArray[ Type ] [ b ] = temp;
  }
}

Shuffle_or_Sort()

void Population_Manager::Shuffle_or_Sort ( unsigned  Type )

protected

This method is used to determine whether the array of animals should be shuffled or sorted.
To do nothing ensure that the BeforeStepActions[] is set appropriately // 0 = Shuffle, 1 = SortX, 2 = SortY, 3 = sortXIndex, 4 = do nothing

Definition at line 1073 of file PopulationManager.cpp.

                                                        {
  switch ( BeforeStepActions[ Type ] ) {
    case 0:
      Shuffle( Type );
      break;
    case 1:
      SortX( Type );
      break;
    case 2:
      SortY( Type );
      break;
    case 3:
      SortXIndex( Type );
      break;
    case 4: // Do nothing
      break;
    case 5: 
      if (g_rand_uni() < double (1/500)) Shuffle( Type );
      break;
    default:
      m_TheLandscape->Warn( "Population_Manager::Shuffle_or_Sort- BeforeStepAction Unknown", NULL );
      exit( 1 );
  }
}

References g_rand_uni.

SortState()

void Population_Manager::SortState ( unsigned  Type )

protected

Sort TheArray w.r.t. the current state attribute

Definition at line 999 of file PopulationManager.cpp.

                                                  {
  sort( TheArray[ Type ].begin(), TheArray[ Type ].end(), CompareState() );
}

SortStateR()

void Population_Manager::SortStateR ( unsigned  Type )

protected

Sort TheArray w.r.t. the current state attribute in reverse order

Definition at line 1008 of file PopulationManager.cpp.

                                                 {
    sort(TheArray[Type].begin(), TheArray[Type].begin()+m_LiveArraySize[Type], CompareStateR());
}

SortX()

void Population_Manager::SortX ( unsigned  Type )

protected

Sort TheArray w.r.t. the m_Location_x attribute

Definition at line 979 of file PopulationManager.cpp.

                                              {
    vector<TAnimal*>::iterator nth = TheArray[Type].begin() + m_LiveArraySize[Type];
    sort( TheArray[ Type ].begin(), nth, CompareX() );
}

SortXIndex()

void Population_Manager::SortXIndex ( unsigned  Type )

protected

Sort TheArray w.r.t. the m_Location_x attribute, and make an indexing array

Definition at line 1027 of file PopulationManager.cpp.

                                                   {
    vector<TAnimal*>::iterator nth = TheArray[Type].begin() + m_LiveArraySize[Type];
    sort(TheArray[Type].begin(), nth, CompareX());
  unsigned s = (unsigned)GetLiveArraySize( Type );
  // Now make the index array to X;
  int counter = 0;
  int x;
  // for each individual
  for ( unsigned i = 0; i < s; i++ ) {
    // Get Next co-ordiated
    x = TheArray[ Type ] [ i ]->Supply_m_Location_x();
    // fill gaps up to x
    while ( counter < x ) IndexArrayX[ Type ] [ counter++ ] = -1;
    if ( x == counter ) {
      IndexArrayX[ Type ] [ counter++ ] = i;
    }
  }
  // Fill up the rest of the array with -1;
  for ( int c = counter; c < 10000; c++ ) {
    IndexArrayX[ Type ] [ c ] = -1;
  }
}

SortY()

void Population_Manager::SortY ( unsigned  Type )

protected

Sort TheArray w.r.t. the m_Location_y attribute

Definition at line 989 of file PopulationManager.cpp.

                                              {
    vector<TAnimal*>::iterator nth = TheArray[Type].begin() + m_LiveArraySize[Type];
    sort(TheArray[Type].begin(), nth, CompareY());
}

SpeciesSpecificReporting()

char * Population_Manager::SpeciesSpecificReporting	(	int	a_species,
		int	a_time
	)

This method handles species specific outputs. This is one place to do it. More commonly this is done in descendent classes

Definition at line 1121 of file PopulationManager.cpp.

                                                                            {
  strcpy(g_str,"");
// Vole Model
  if ( a_species == 1 ) {
/*
// The next lines are obselete code from genetic simulations
float MeanNoAlleles;
    float MeanHO;
    float MeanHE;
    unsigned size;
 
    if ( m_time % ( 365 * 24 * 60 ) == 0 ) // End of year
    {
 
      // empty the GenStruc data
      for ( int ProbeNo = 0; ProbeNo < ( int )m_NoProbes; ProbeNo++ ) {
        fprintf( m_GeneticsFile, "%d ", m_time );
        int TotalSize = 0;
        m_AManager->AlFreq->Flush();
        for ( unsigned listindex = 0; listindex <= 1; listindex++ ) {
          size = 0;
          m_AManager->TheGeneticProbe( listindex, ProbeNo, size );
          TotalSize += size;
        }
        if ( TotalSize > 0 ) {
          m_AManager->AlFreq->CalcAF();
          m_AManager->AlFreq->CalcNoAlleles();
          m_AManager->AlFreq->CalcHE();
          m_AManager->AlFreq->CalcHO( TotalSize );
        }
        // Get the means
        // For N alleles
        int NA = 0;
        float NHO = 0;
        float NHE = 0;
        for ( int l = 0; l < 16; l++ ) {
          NA += m_AManager->AlFreq->SupplyNoAlleles( l );
        }
        MeanNoAlleles = ( float )NA / 16.0;
        for ( int l = 0; l < 16; l++ ) {
          NHO += m_AManager->AlFreq->SupplyHO( l );
        }
        MeanHO = NHO / 16.0;
        for ( int l = 0; l < 16; l++ ) {
          NHE += m_AManager->AlFreq->SupplyHE( l );
        }
        MeanHE = NHE / 16.0;
 
        // Do some output
        // Output is to two files, the genetics file and the AllelerequencyFile
        fprintf( m_GeneticsFile, "%2.2f ", MeanNoAlleles );
        fprintf( m_GeneticsFile, "%1.3f ", MeanHO );
        fprintf( m_GeneticsFile, "%1.3f ", MeanHE );
        for ( int l = 0; l < 16; l++ ) {
          fprintf( m_GeneticsFile, "%04i ", m_AManager->AlFreq->SupplyNoAlleles( l ) );
        }
        for ( int l = 0; l < 16; l++ ) {
          fprintf( m_GeneticsFile, "%1.3f ", m_AManager->AlFreq->SupplyHO( l ) );
        }
        for ( int l = 0; l < 16; l++ ) {
          fprintf( m_GeneticsFile, "%1.3f ", m_AManager->AlFreq->SupplyHE( l ) );
        }
        fprintf( m_GeneticsFile, "\n" );
        fprintf( m_AlleleFreqsFile, "%d ", m_time );
        for ( int l = 0; l < 16; l++ ) {
          for ( int al = 0; al < 4; al++ ) {
            fprintf( m_AlleleFreqsFile, "%1.3f ", m_AManager->AlFreq->SupplyAF( l, al ) );
          }
        }
        fprintf( m_AlleleFreqsFile, "\n" );
      }
      // make sure progress reaches the disk
      fflush( m_GeneticsFile );
      fflush( m_AlleleFreqsFile );
    }
 
    if ( cfg_UseEasyPop.value()) {
      int targettime=a_time % ( 365 * 100 );
      if ( (  targettime == 59 ) ||(targettime == 181)||(targettime ==304)||(targettime ==59+365)||(targettime ==181+365)||(targettime ==304+365)) {
          for ( unsigned listindex = 0; listindex <= 1; listindex++ ) {
            GeneticsResultsOutput( m_EasyPopRes, listindex);
        }
        fflush( m_EasyPopRes );
      }
    }
*/
    /* Three times a year reporting
    if ( m_time % 365 == 60 ) ProbeReportNow( m_time );
    if ( m_time % 365 == 152 ) ProbeReportNow( m_time );
    if ( m_time % 365 == 273 ) ProbeReportNow( m_time ); */
    ProbeReport( a_time );
#ifdef __SpecificPesticideEffectsVinclozolinLike__
    ImpactProbeReport( a_time );
#endif
#ifdef __WithinOrchardPesticideSim__
    ImpactProbeReport( a_time );
#endif
 
  }
  // Skylark Model
  else if ( a_species == 0 ) {
    int No;
    int a_day = a_time % 365;
    if ( a_time % 365 == 364 )
    {
      //Write the Breeding Attempts Probe
      int BreedingFemales, YoungOfTheYear, TotalPop, TotalFemales, TotalMales, BreedingAttempts;
      No = TheBreedingSuccessProbe( BreedingFemales, YoungOfTheYear, TotalPop, TotalFemales, TotalMales, BreedingAttempts );
      float bs = 0;
      if ( BreedingFemales > 0 ) {
        bs = No / ( float )BreedingFemales; //bs = successful breeding attempt per attempting to breed female
      }
      BreedingSuccessProbeOutput( bs, BreedingFemales, YoungOfTheYear, TotalPop,
           TotalFemales, TotalMales, a_time, BreedingAttempts );
    }
    if ( a_day == 152 ) {
      // Need to fill in the landscape from 1st June, it will change before
      // the count of fledgelings is needed
      m_TheLandscape->FillVegAreaData();
    }
    if ( a_day == 197 ) {
      for ( int ProbeNo = 0; ProbeNo < m_NoProbes; ProbeNo++ ) {
        No = TheFledgelingProbe();
        // Do some output
        FledgelingProbeOutput( No, a_time );
      }
    }
#ifdef __SKPOM
    // This is clunky but for purposes of validation we want probes throughout the year
    // First get the breeding pairs data.
    BreedingPairsOutput(a_day);
#else
    ProbeReport( a_time );
#endif
  }
  else return ProbeReport( a_time );
  return g_str;
}

References g_str.

StepFinished()

bool Population_Manager::StepFinished ( void  )

protectedvirtual

Overrides the population manager StepFinished - there is no chance that hunters do not finish a step behaviour.

Returns true if and only if all objects have finished the current step

Definition at line 498 of file PopulationManager.cpp.

                                            {
  for ( unsigned listindex = 0; listindex < TheArray.size(); listindex++ ) {
      for (unsigned j = 0; j < (unsigned)GetLiveArraySize( listindex ); j++) {
      if ( TheArray[ listindex ] [ j ]->GetStepDone() == false ) {
        return false;
      }
    }
  }
  return true;
}

SupplyAnimalPtr()

TAnimal* Population_Manager::SupplyAnimalPtr ( int  a_index, int  a_animal  )

inline

Returns the pointer indexed by a_index and a_animal. Note NO RANGE CHECK.

Definition at line 465 of file populationmanager.h.

                                                        {
        return TheArray[a_index][a_animal];
    }

References TheArray.

SupplyCovPosx()

virtual int Population_Manager::SupplyCovPosx ( int  )

inlinevirtual

Definition at line 626 of file populationmanager.h.

                                   {
        return 0;
    }

SupplyCovPosy()

virtual int Population_Manager::SupplyCovPosy ( int  )

inlinevirtual

Definition at line 629 of file populationmanager.h.

                                   {
        return 0;
    }

SupplyListIndexSize()

unsigned Population_Manager::SupplyListIndexSize ( )

inline

Definition at line 468 of file populationmanager.h.

                                   {
        return (unsigned)TheArray.size();
    }

References TheArray.

SupplyListName()

const char* Population_Manager::SupplyListName ( int  i )

inline

Definition at line 478 of file populationmanager.h.

                                      {
            return m_ListNames[i];
    }

References m_ListNames.

SupplyListNameLength()

int Population_Manager::SupplyListNameLength ( )

inline

Definition at line 461 of file populationmanager.h.

                               {
        return m_ListNameLength;
    }

References m_ListNameLength.

SupplyListSize()

unsigned Population_Manager::SupplyListSize ( unsigned  listindex )

inline

Definition at line 471 of file populationmanager.h.

                                                {
        return (unsigned)TheArray[listindex].size();
    }

References TheArray.

SupplyLocXY()

virtual void Population_Manager::SupplyLocXY ( unsigned  listindex, unsigned  j, int &  x, int &  y  )

inlinevirtual

Definition at line 493 of file populationmanager.h.

                                                                               {
        x = TheArray[listindex][j]->Supply_m_Location_x();
        y = TheArray[listindex][j]->Supply_m_Location_y();
    }

References TheArray.

SupplyPegPosx()

virtual int Population_Manager::SupplyPegPosx ( int  )

inlinevirtual

Definition at line 620 of file populationmanager.h.

                                   {
        return 0;
    }

SupplyPegPosy()

virtual int Population_Manager::SupplyPegPosy ( int  )

inlinevirtual

Definition at line 623 of file populationmanager.h.

                                   {
        return 0;
    }

SupplySimH()

int Population_Manager::SupplySimH ( )

inline

Definition at line 455 of file populationmanager.h.

                     {
        return SimH;
    }

References SimH.

SupplySimW()

int Population_Manager::SupplySimW ( )

inline

Definition at line 452 of file populationmanager.h.

                     {
        return SimW;
    }

References SimW.

SupplyState()

int Population_Manager::SupplyState ( unsigned  listindex, unsigned  j  )

inline

IntArray100 * SupplyStateList() { return & StateList; }

Definition at line 490 of file populationmanager.h.

                                                    {
        return TheArray[listindex][j]->WhatState();
    }

References TheArray.

SupplyStateNames()

const char* Population_Manager::SupplyStateNames ( int  i )

inline

Definition at line 497 of file populationmanager.h.

                                        {
        return StateNames[i];
    }

References StateNames.

SupplyStateNamesLength()

unsigned Population_Manager::SupplyStateNamesLength ( )

inline

Definition at line 500 of file populationmanager.h.

                                      {
        return StateNamesLength;
    }

References StateNamesLength.

SupplyStepSize()

int Population_Manager::SupplyStepSize ( )

inline

Definition at line 449 of file populationmanager.h.

                         {
        return m_StepSize;
    }

References m_StepSize.

TheAOROutputProbe()

void Population_Manager::TheAOROutputProbe ( )

virtual

This method must be overridden in descendent classes

Reimplemented in Rabbit_Population_Manager.

Definition at line 924 of file PopulationManager.cpp.

                                           {
}

TheBreedingFemalesProbe()

virtual int Population_Manager::TheBreedingFemalesProbe ( int  )

inlinevirtual

Definition at line 643 of file populationmanager.h.

                                             {
        return 0;
    }

TheBreedingSuccessProbe()

virtual int Population_Manager::TheBreedingSuccessProbe ( int &  , int &  , int &  , int &  , int &  , int &    )

inlinevirtual

Definition at line 651 of file populationmanager.h.

                                                                                  {
        return 0;
    }

TheFledgelingProbe()

virtual int Population_Manager::TheFledgelingProbe ( )

inlinevirtual

Definition at line 646 of file populationmanager.h.

                                     {
        return 0;
    }

TheGeneticProbe()

virtual void Population_Manager::TheGeneticProbe ( unsigned  , int  , unsigned &    )

inlinevirtual

Definition at line 656 of file populationmanager.h.

                                                            {
    }

TheReallyBigOutputProbe()

void Population_Manager::TheReallyBigOutputProbe ( )

virtual

This method must be overridden in descendent classes

Definition at line 913 of file PopulationManager.cpp.

                                                 {
}

TheRipleysOutputProbe()

void Population_Manager::TheRipleysOutputProbe ( FILE *  a_prb )

virtual

This method must be overridden in descendent classes

Definition at line 918 of file PopulationManager.cpp.

                                                      {
}

Member Data Documentation

AOROutputPrb

ofstream* Population_Manager::AOROutputPrb

protected

Definition at line 581 of file populationmanager.h.

BeforeStepActions

unsigned Population_Manager::BeforeStepActions[12]

protected

Definition at line 542 of file populationmanager.h.

IndexArrayX

int Population_Manager::IndexArrayX[5][10000]

Definition at line 509 of file populationmanager.h.

lamdagrid

long int Population_Manager::lamdagrid[2][257][257]

protected

Definition at line 597 of file populationmanager.h.

Referenced by LamdaBirth(), LamdaClear(), and LamdaDeath().

m_AlleleFreqsFile

FILE* Population_Manager::m_AlleleFreqsFile

protected

Definition at line 528 of file populationmanager.h.

m_AOR_Probe

AOR_Probe* Population_Manager::m_AOR_Probe

protected

Definition at line 526 of file populationmanager.h.

Referenced by Rabbit_Population_Manager::TheAOROutputProbe().

m_catastrophestartyear

int Population_Manager::m_catastrophestartyear

protected

Definition at line 532 of file populationmanager.h.

m_EasyPopRes

FILE* Population_Manager::m_EasyPopRes

protected

Definition at line 529 of file populationmanager.h.

m_GeneticsFile

FILE* Population_Manager::m_GeneticsFile

protected

Definition at line 527 of file populationmanager.h.

m_ListNameLength

unsigned Population_Manager::m_ListNameLength

protected

Definition at line 538 of file populationmanager.h.

Referenced by Rabbit_Population_Manager::Rabbit_Population_Manager(), and SupplyListNameLength().

m_ListNames

const char* Population_Manager::m_ListNames[32]

protected

Definition at line 537 of file populationmanager.h.

Referenced by Rabbit_Population_Manager::Rabbit_Population_Manager(), and SupplyListName().

m_LiveArraySize

vector<unsigned> Population_Manager::m_LiveArraySize

protected

Definition at line 524 of file populationmanager.h.

Referenced by GetLiveArraySize(), and IncLiveArraySize().

m_NoProbes

int Population_Manager::m_NoProbes

protected

Definition at line 525 of file populationmanager.h.

Referenced by SetNoProbes().

m_population_type

TTypesOfPopulation Population_Manager::m_population_type

protected

Definition at line 580 of file populationmanager.h.

Referenced by GetPopulationType().

m_SeasonNumber

int Population_Manager::m_SeasonNumber

protected

Holds the season number. Used when running goose and hunter sims.

Definition at line 544 of file populationmanager.h.

Referenced by GetSeasonNumber().

m_SimulationName

char Population_Manager::m_SimulationName[255]

Definition at line 513 of file populationmanager.h.

Referenced by Rabbit_Population_Manager::Rabbit_Population_Manager().

m_StepSize

int Population_Manager::m_StepSize

protected

Definition at line 533 of file populationmanager.h.

Referenced by SupplyStepSize().

m_TheLandscape

Landscape* Population_Manager::m_TheLandscape

Definition at line 515 of file populationmanager.h.

Referenced by Rabbit_Population_Manager::AssessPctForage(), Rabbit_Population_Manager::AssignStaticVariables(), Rabbit_Population_Manager::CheckForRabbitBreedingConditions(), Rabbit_Population_Manager::ClassifyHabitat(), Rabbit_Population_Manager::DoFirst(), Rabbit_Population_Manager::DoLast(), Rabbit_Population_Manager::LoadWarrenLocations(), Rabbit_Population_Manager::NatalDispersalRecordOutput(), Rabbit_Population_Manager::PesticideDeathRecordOutput(), Rabbit_Population_Manager::PreProcessWarrenLocations(), Rabbit_Population_Manager::Rabbit_Population_Manager(), Rabbit_Population_Manager::ReproOutputRecordOutput(), Rabbit_Population_Manager::WarrenLegalPos(), and Rabbit_Population_Manager::WarrenOccupancyRecordOutput().

ProbesSet

bool Population_Manager::ProbesSet

Definition at line 514 of file populationmanager.h.

ReallyBigOutputPrb

FILE* Population_Manager::ReallyBigOutputPrb

protected

Definition at line 595 of file populationmanager.h.

RipleysOutputPrb

FILE* Population_Manager::RipleysOutputPrb

protected

Definition at line 582 of file populationmanager.h.

RipleysOutputPrb1

FILE* Population_Manager::RipleysOutputPrb1

protected

Definition at line 583 of file populationmanager.h.

RipleysOutputPrb10

FILE* Population_Manager::RipleysOutputPrb10

protected

Definition at line 592 of file populationmanager.h.

RipleysOutputPrb11

FILE* Population_Manager::RipleysOutputPrb11

protected

Definition at line 593 of file populationmanager.h.

RipleysOutputPrb12

FILE* Population_Manager::RipleysOutputPrb12

protected

Definition at line 594 of file populationmanager.h.

RipleysOutputPrb2

FILE* Population_Manager::RipleysOutputPrb2

protected

Definition at line 584 of file populationmanager.h.

RipleysOutputPrb3

FILE* Population_Manager::RipleysOutputPrb3

protected

Definition at line 585 of file populationmanager.h.

RipleysOutputPrb4

FILE* Population_Manager::RipleysOutputPrb4

protected

Definition at line 586 of file populationmanager.h.

RipleysOutputPrb5

FILE* Population_Manager::RipleysOutputPrb5

protected

Definition at line 587 of file populationmanager.h.

RipleysOutputPrb6

FILE* Population_Manager::RipleysOutputPrb6

protected

Definition at line 588 of file populationmanager.h.

RipleysOutputPrb7

FILE* Population_Manager::RipleysOutputPrb7

protected

Definition at line 589 of file populationmanager.h.

RipleysOutputPrb8

FILE* Population_Manager::RipleysOutputPrb8

protected

Definition at line 590 of file populationmanager.h.

RipleysOutputPrb9

FILE* Population_Manager::RipleysOutputPrb9

protected

Definition at line 591 of file populationmanager.h.

SimH

int Population_Manager::SimH

Definition at line 511 of file populationmanager.h.

Referenced by Rabbit_Population_Manager::CreateLocalWarrenNetworkLists(), Rabbit_Population_Manager::DoFirst(), Rabbit_Population_Manager::FindClosestWarren(), Rabbit_Population_Manager::PreProcessWarrenLocations(), Rabbit_Population_Manager::Rabbit_Population_Manager(), and SupplySimH().

SimHH

unsigned Population_Manager::SimHH

Definition at line 512 of file populationmanager.h.

SimW

int Population_Manager::SimW

Definition at line 511 of file populationmanager.h.

Referenced by Rabbit_Population_Manager::DoFirst(), Rabbit_Population_Manager::FindClosestWarren(), Rabbit_Population_Manager::PreProcessWarrenLocations(), Rabbit_Population_Manager::Rabbit_Population_Manager(), and SupplySimW().

SimWH

unsigned Population_Manager::SimWH

Definition at line 512 of file populationmanager.h.

StateNames

const char* Population_Manager::StateNames[100]

protected

Definition at line 531 of file populationmanager.h.

Referenced by SupplyStateNames().

StateNamesLength

unsigned Population_Manager::StateNamesLength

protected

Definition at line 535 of file populationmanager.h.

Referenced by SupplyStateNamesLength().

TestFile

FILE* Population_Manager::TestFile

protected

Definition at line 539 of file populationmanager.h.

TestFile2

FILE* Population_Manager::TestFile2

protected

Definition at line 540 of file populationmanager.h.

TheArray

vector< TListOfAnimals > Population_Manager::TheArray

protected

Definition at line 534 of file populationmanager.h.

Referenced by Rabbit_Population_Manager::CreateLocalWarrenNetworkLists(), Rabbit_Population_Manager::CreateObjects(), Rabbit_Population_Manager::DoFirst(), Rabbit_Population_Manager::FindClosestWarren(), IsLast(), Rabbit_Population_Manager::PreProcessWarrenLocations(), Rabbit_Population_Manager::SaveWarrenLocations(), Rabbit_Population_Manager::SupplyAllBigRabbits(), SupplyAnimalPtr(), SupplyListIndexSize(), SupplyListSize(), SupplyLocXY(), SupplyState(), Rabbit_Population_Manager::WarrenLegalPos(), Rabbit_Population_Manager::WarrenOccupancyRecordOutput(), and Rabbit_Population_Manager::~Rabbit_Population_Manager().

TheProbe

probe_data* Population_Manager::TheProbe[100]

Definition at line 510 of file populationmanager.h.

---

The documentation for this class was generated from the following files:

• C:/Repo/ALMaSS_all/BatchALMaSS/populationmanager.h
• C:/Repo/ALMaSS_all/BatchALMaSS/PopulationManager.cpp